This package is considered a duplicate. The official version of this package is found at:https://ucd-serg.r-universe.dev/serodynamics

Package: serodynamics 0.1.0

Samuel Schildhauer

serodynamics: Modeling Longitudinal Antibody Responses to Infection

Implements Bayesian hierarchical models for estimating antibody kinetic parameters from longitudinal serological data. Fits two-phase within-host models capturing antibody rise, peak, and decay following pathogen infection, using 'JAGS' for posterior inference. Designed as the upstream companion to the 'serocalculator' package for end-to-end seroepidemiological analysis. Methods are described in Teunis and colleagues (2016) <doi:10.1016/j.epidem.2016.04.001> and Teunis and van Eijkeren (2020) <doi:10.1002/sim.8578>.

Authors:Peter Teunis [aut, cph], Samuel Schildhauer [aut, cre], Kwan Ho Lee [aut], Kristen Aiemjoy [aut], Douglas Ezra Morrison [aut]

serodynamics_0.1.0.tar.gz
serodynamics_0.1.0.zip(r-4.7-any)serodynamics_0.1.0.zip(r-4.6-any)
serodynamics_0.1.0.tar.gz(r-4.7-any)serodynamics_0.1.0.tar.gz(r-4.6-any)
serodynamics_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
serodynamics/json (API)

# Install 'serodynamics' in R:

install.packages('serodynamics', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ucd-serg/serodynamics/issues

Pkgdown/docs site:https://ucd-serg.github.io

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

nepal_sees - SEES Typhoid data
nepal_sees_jags_output - SEES Typhoid run_mod jags output

On CRAN:

jags cpp

2.70 score 8 scripts 235 downloads 20 exports 59 dependencies

Last updated from:cd0b7fc01f. Checks:6 OK. Indexed: no.

Target	Result	Time
linux-devel	OK	174
source / vignettes	OK	243
linux-release	OK	169
windows-devel	OK	120
windows-release	OK	131
wasm-release	OK	143

Exports:as_case_data autoplot expect_snapshot_data get_biomarker_levels get_biomarker_names_var initsfunction load_data plot_jags_dens plot_jags_effect plot_jags_Rhat plot_jags_trace plot_predicted_curve post_summ postprocess_jags_output prep_data prep_priors run_mod serodynamics_example sim_case_data sim_n_obs

Dependencies:and bit bit64 cli clipr coda codetools cpp11 crayon digest doParallel dplyr farver forcats foreach generics GGally ggmcmc ggplot2 ggstats glue gtable haven hms isoband iterators labeling labelled lattice lifecycle magrittr MASS patchwork pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp readr rlang rngtools runjags S7 scales serocalculator stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

dobson

Rendered fromdobson.Rmdusingknitr::rmarkdown

Last update: 2026-06-02
Started: 2026-06-02

Help page	Topics
Convert data into 'case_data'	as_case_data
Plot case data	autoplot.case_data
JAGS chain initialization function	initsfunction
load and format data	load_data
SEES Typhoid data	nepal_sees
SEES Typhoid run_mod jags output	nepal_sees_jags_output
Density Plot Diagnostics	plot_jags_dens
Plot Effective Sample Size Diagnostics	plot_jags_effect
Rhat Plot Diagnostics	plot_jags_Rhat
Trace Plot Diagnostics	plot_jags_trace
Generate Predicted Antibody Response Curves (Median + 95% CI)	plot_predicted_curve
Summary Table of Jags Posterior Estimates	post_summ
Postprocess JAGS output	postprocess_jags_output
prepare data for JAGs	prep_data
Prepare priors	prep_priors
Run Jags Model	run_mod
Get path to an example file	serodynamics_example
Simulate longitudinal case follow-up data from a homogeneous population	sim_case_data

Package: serodynamics 0.1.0

serodynamics: Modeling Longitudinal Antibody Responses to Infection

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)